I assume you are referring to the data that he gave to the Konaha ninja? With Orochimaru gone, the only thing left is to carry out his previous wishes - which in some way include the use of such information being given to Naruto. He is still considered a villain in my opinion, though him "helping" our protagonists must be for an ulterior motive.
His own. Or rather, trying to figure out what his own side would be, exploring the options that he has while he's at it. Sure, he follows Orochimaru and professes to being taken in by the Sannin's grand ideals, but I still think that it is a matter of Kabuto not really having anything else to latch onto. All he knew since he was a child was spying after all, even learning to be a medic nin was part of his roll as a spy in Konoha.